moebiusband/MD-Bench
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
333 Commits 8 Branches 0 Tags 3.4 MiB
da3b1dd53f
Commit Graph

333 Commits

This Branch
This Branch
All Branches
Author SHA1 Message Date
Rafael Ravedutti
eedcc97e4a Remove segfaults 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-28 15:18:54 +01:00
Rafael Ravedutti
a119fcdfdd Fix some segfaults and add function to update single atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-27 03:07:31 +01:00
Rafael Ravedutti
aa0f4048d0 Rename default directory to lammps and reorganize gromacs variant steps 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-25 21:00:11 +01:00
Rafael Ravedutti
cbe42b8149 Fix errors to make gromacs approach compilable so far 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-25 12:19:28 +01:00
Rafael Ravedutti
6291709ae7 Add first draft code with GROMACS approach 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-25 00:43:10 +01:00
Rafael Ravedutti
72730bc27b Update Makefile and config.mk 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-17 14:16:39 +01:00
Rafael Ravedutti
df09c2861e Add first version with more than one optimization scheme 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-17 14:15:02 +01:00
Rafael Ravedutti
489e7ee9d3 Update .gitignore 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-17 11:46:57 +01:00
Rafael Ravedutti
165335cea0 Update compilation flags for all available compilers 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-17 11:40:44 +01:00
Rafael Ravedutti
35c110155e Separate tracing from force computation and fix stubbed version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-12-01 00:07:45 +01:00
Rafael Ravedutti
bb21a885a1 Add new setups for Copper melting with LJ and EAM 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-30 01:33:55 +01:00
Rafael Ravedutti
f7010113bf Include commented timestamping on asm 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-10 14:39:44 +01:00
Rafael Ravedutti
841dfb9490 Fix data types for rdr and rdrho 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-09 20:36:23 +01:00
Rafael Ravedutti
f8b9a095cf Add working version of force.s 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-09 01:23:15 +01:00
Rafael Ravedutti
b2dada6179 Fix param references and assembler errors for force.s 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-09 00:05:42 +01:00
Rafael Ravedutti
d8c8733cb2 Update asm force again 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-08 23:32:24 +01:00
Rafael Ravedutti
cf7ea1460c Update asm version to be integrated 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-08 22:31:58 +01:00
Rafael Ravedutti
9b615cf0b3 Update force kernel to be integrated 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-08 14:05:29 +01:00
Rafael Ravedutti
ec556eb117 Add EAM without explicit types and update fp for PBC atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-11-03 00:57:24 +01:00
Rafael Ravedutti
0f1e824507 Fix integration with mass and add VTK output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-29 16:52:19 +02:00
Rafael Ravedutti
d9c9cba12d Set EAM parameters for same case as miniMD 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-27 01:38:56 +02:00
Rafael Ravedutti
70cc6aeb19 Add first working version of EAM 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 13:55:14 +02:00
Rafael Ravedutti
7db14b2ffe Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2021-10-26 12:34:43 +02:00
Rafael Ravedutti
d7056f09f4 Fix illegal accesses due to invalid type of ghost atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 12:34:35 +02:00
Jan Eitzinger
70e24d7c2c Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2021-10-26 09:16:31 +02:00
Jan Eitzinger
3c3d27b48a Introduce separate version for traced force routine. 2021-10-26 09:11:17 +02:00
Rafael Ravedutti
99d6a4bdd8 Fix Funcfl reference to avoid segfaults 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 01:40:02 +02:00
Rafael Ravedutti
40ddc9ad50 Fix errors introduced by last changes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 01:19:11 +02:00
Rafael Ravedutti
2dac10469c Add EAM force field 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-26 00:40:39 +02:00
Rafael Ravedutti
9d16bb46c8 Include average neighbors and SIMD iterations per atom on stats 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-20 22:43:08 +02:00
Rafael Ravedutti
557c5e4d3f IUpdate logbook again and do not check for variant on ATOMS_LOOP_RUNS effect 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-14 00:46:30 +02:00
Rafael Ravedutti
40bbaac078 Add hardware information on logbook 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-13 22:27:34 +02:00
Rafael Ravedutti
c46e4ee4df Include ATOMS_LOOP_RUNS option in config.mk file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-12 23:35:58 +02:00
Rafael Ravedutti
43ba28e130 Add ATOMS_LOOP_RUNS option and statistics to stub variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-12 22:39:54 +02:00
Rafael Ravedutti
55d346510e Compute statistics, useful data volume and cycles per SIMD iteration 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-12 15:04:08 +02:00
Rafael Ravedutti
f295f54fca Add useful data volume calculation for force kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-11 16:57:02 +02:00
Rafael Ravedutti
4e0390404a Add correct version (without traces) of CACHES_PMC results with and without force calculation on casclakesp2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-06 16:08:46 +02:00
Rafael Ravedutti
b1f8e91f0f Add cache measurements for versions with and without force computation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-04 18:13:17 +02:00
Rafael Ravedutti
749c4d55ab Provide trace output for all reneighboring steps 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-10-04 16:47:07 +02:00
Rafael Ravedutti
2889577a3b Add neighbor lists capacity to index tracer file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-10 17:28:59 +02:00
Rafael Ravedutti
b8d71090aa Add number of atoms in index tracer file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-10 16:43:51 +02:00
Rafael Ravedutti
6b75c158d6 Include atom reference on index tracer and add only_mem ASM version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-10 01:19:26 +02:00
Rafael Ravedutti
9d79f0248f Add config option to switch between asm syntaxes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-08-09 21:37:18 +02:00
Rafael Ravedutti
effd961f29 Add cache sets histogram script, update gather plot script and add results for icx32 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-29 17:01:30 +02:00
Rafael Ravedutti
57041ceed2 Add likwid-perfctr run with CACHES_PMC for 1 timestep on casclakesp2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-16 00:24:43 +02:00
Rafael Ravedutti
8e1542c87d Sort elements within vector to fix distance calculation on index tracer 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-15 23:51:00 +02:00
Rafael Ravedutti
d97fc577b0 Add first version of index and distance tracer 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-09 23:49:14 +02:00
Rafael Ravedutti
e6062e8f79 Update script to plot stubbed data and add results for casclakesp2 with AoS 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-03 03:07:35 +02:00
Rafael Ravedutti
eef44e97d7 Update cache settings for casclakesp2 and results 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-02 02:57:31 +02:00
Rafael Ravedutti
4bde1944cf Update script for plotting gather data and AOS results for casclakesp2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2021-07-01 20:02:59 +02:00